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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatctgccgattacttgtctgcgtttacatttctgtcgttgaatgcttgattatgatttaaaccaactctcctcatcccctgggtgagaatgtgagatgttgctgcatcctaaaacccgcatgctcattattgtacatgttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG

Basic information

species Oryza sativa
transcript LOC_Os02g56850.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g56850.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G806449_T02 (Zea mays), 3'ss of exon 3
gtaagcatctgccgattacttgtctgcgtttacatttctgtcgttgaatgcttgattatgatttaaaccaactctcctcatcccctgggtgagaatgtgagatgttgctgcatcctaaaacccgcatgctcattattgtaca--tgttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG
|||||||||| |    || |||| | ||  | |||||||         |||||  | |  |  |  | | | ||| ||              | || |      |  || ||| |||||  |  |||| |||| ||  |     | |||| |||| || |||||||||||||| || |||||||||||||| ||||||||| |||| ||||| ||||||||||||
gtaagcatctcc----tagttgttttcg--tgcatttctc-------gtgcttactcaaaacatgcagctattctgcttg------------gtatat------taactacattctaaa-tcgacatgttcataatgattttattattgtcctagTTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATCATTCCGTGGAGAATTTGAG

upper sequence: LOC_Os02g56850.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv05s0051g00870.t01 (Vitis vinifera), 3'ss of exon 4
gtaagcatctgccgattacttgtctgcgtttacatttctgtcgttgaatgcttgattatgatttaaaccaactctcctcatcccctgggtgagaatgtgagatgttgctgcatcctaaaacccgcatgctcattattgtacatgttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG
                                            ||  || | |||  ||| |||    ||   |  | ||  |     ||| | | ||| |     ||  |   | | |    ||||     |    |    ||| ||| |||||||| || ||||||||||| |||||||||||  ||||||||||  |||||||  | || ||| |||||
------------------------------------------tctgtttgttagatgttgaattag--taatgatggttattgc--aaatgaaattctgaaa-----ctaaaatttcatattgtcatgacgtctcacatctgggtt-tgc-agGTGTGTTATCCGTGGTTGTGTTCCTAAAAAGATTTTGGTGTATGGAGCATCTTTTAGAGGTGAAATTGAG
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|88726007|gb|CI749662.1|CI749662
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC                         GTGTGTGATACGTGGTTGTGT
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTGT
EST: gi|88726529|gb|CI750184.1|CI750184
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC                         GTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
EST: gi|88722054|gb|CI745381.1|CI745381
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC                         GTGTGTGATACGTGGTTGTGTGCCTA
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTGTGCCTA
EST: gi|88395150|gb|CI609466.1|CI609466
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGACGGCATGGTGGGAC                         GTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
EST: gi|58686599|gb|CK075286.1|CK075286
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC                         GTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
EST: gi|88416046|gb|CI594158.1|CI594158
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC                         GTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
EST: gi|29675048|gb|CB671323.1|CB671323
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC                         GTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
EST: gi|2443112|gb|C74883.1|C74883
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC                         GTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
EST: gi|88694888|gb|CI738926.1|CI738926
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC                         GTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
EST: gi|88723894|gb|CI745591.1|CI745591
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC                         GTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
EST: gi|426418|gb|D22281.1|D22281
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC                         GTGTGTNATACGTGGTTGTGTNCCTAAAAAGATACTGGTGTATGGTTCATC
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
EST: gi|88718629|gb|CI742139.1|CI742139
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC                         GTGTGTGATACGTGGTTGTG
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagatgttgctgcatcctaaaacccgcatgctcattattgtacatgttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG
              tcctaaa  putative branch site (score: 2)
                                 attattgta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcatctgccgattacttgtctgcgtttacatttctgtcgttgaatgcttgattatgatttaaaccaactctcctcatcccctgggtgagaatgtgagatgttgctgcatcctaaaacccgcatgctcattattgtacatgttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG

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